Search Results (24)

Seagrass meadows are recognized for their ecological importance, yet their influence on microbial community structure remains insufficiently characterized. This study examined the effects of seagrass presence on microbial assemblages in a subtropical coastal environment by comparing seagrass habitats to adjacent unvegetated sediments. Microbial abundances, including viruses, bacteria, picophytoplankton (Synechococcus spp. and picoeukaryotes), and heterotrophic nanoflagellates, were quantified using flow cytometry. Viral concentrations were significantly higher in seagrass treatments (2.4–9.2 × 10⁶ viruses mL⁻¹) than in controls (0.6–2.0 × 10⁶ viruses mL⁻¹), while bacterial abundances were slightly lower in seagrass treatments (5.1–16.0 × 10⁵ cells mL⁻¹) than in controls (7.9–16.6 × 10⁵ cells mL⁻¹). As a result, the virus-to-bacteria ratio (VBR) was significantly elevated in seagrass habitats, suggesting enhanced viral regulation of bacterial populations. Additionally, picophytoplankton and heterotrophic nanoflagellates increased in seagrass incubations, with strong correlations indicating that nanoflagellates are likely major grazers of picophytoplankton. These results highlight the role of seagrass habitats in modulating microbial interactions and emphasize the need to consider habitat-specific characteristics when evaluating microbial dynamics and biogeochemical processes in coastal systems. Full article

Kuibyshev Reservoir, the largest in the Volga basin, is poorly covered by modern molecular studies. The results of a metabarcoding study of pro- and eukaryotic microbial plankton in its lower section during the summer period are presented. Bacterioplankton composition was typical for most temperate freshwater bodies and characterized by the dominance of cyanobacteria, Pseudomonadota, Bacteroidota, Actinomycetota, and PVC superphylum (Verrucomicrobiota and Planctomycetota), with a somewhat increased proportion of the latter. The protist community was dominated by Cryptista, principally phototrophic, and various ciliates. Several picoeukaryotic groups were newly detected in the reservoir. A relationship between the composition of both bacterioplankton and protist communities and the stage of phytoplankton succession, including the cyanobacterial bloom, was observed. Some inconsistency between the cyanobacterial bloom phase and the structure of other parts of the microbial plankton is obviously due to some temporal delay, spatial station position, and inflow from tributaries. Heterotrophic bacterioplankton indicator species of the main bloom stage include OTUs representing both the phycosphere of colonial cyanobacteria and free-living species. Among the protists, sessile ciliates benefit most from plenty of substrates for colonization, while cyanobacterial grazers and parasites were minor. Overall, the cyanobacterial bloom creates new niches for the plankton community and significantly modifies its structure. Full article

In this communication, we present an innovative approach leveraging advanced Machine Learning (ML) and Artificial Intelligence (AI) techniques, specifically the Non-Negative Matrix Factorization (NMF) method, to analyze downward and upward light spectra collected by Hyperspectral Ocean Color Radiometer (HyperOCR, HOCR) sensors in the water column. Our work focuses on the development of a robust and efficient tool for unraveling the structure and activities of natural microbial assemblages in the ocean. By applying the NMF method to HyperOCR data, we successfully extracted five spectral signatures, representing unique patterns in the data. These signatures were instrumental in predicting the abundances of various microbial components, including bacteria, heterotrophic nanoflagellates, and picoeukaryotes, showcasing the potential of ML and AI in advancing oceanographic studies. To validate these methods, the study area included a shallow coastal area under the influence of freshwater inflow and an open offshore area with a depth of 100 m. The study sites in coastal and offshore waters (Kaštela Bay and Stončica Vis, respectively) had significantly different hydrographic and microbiological characteristics. Kaštela Bay had lower temperatures and salinity than the site on Vis. We have demonstrated prediction of the structure of the microbial community through application of different AI and ML methods with specific HOCR sensors. Full article

With the birth of next-generation sequencing (NGS) technology, genomic data in public databases have increased exponentially. Unfortunately, exogenous contamination or intracellular parasite sequences in assemblies could confuse genomic analysis. Meanwhile, they can provide a valuable resource for studies of host-microbe interactions. Here, we used a strategy based on DNA barcodes to scan protistan contamination in the GenBank WGS/TSA database. The results showed a total of 13,952 metazoan/animal assemblies in GenBank, where 17,036 contigs were found to be protistan contaminants in 1507 assemblies (10.8%), with even higher contamination rates in taxa of Cnidaria (150/281), Crustacea (237/480), and Mollusca (107/410). Taxonomic analysis of the protists derived from these contigs showed variations in abundance and evenness of protistan contamination across different metazoan taxa, reflecting host preferences of Apicomplexa, Ciliophora, Oomycota and Symbiodiniaceae for mammals and birds, Crustacea, insects, and Cnidaria, respectively. Finally, mitochondrial proteins COX1 and CYTB were predicted from these contigs, and the phylogenetic analysis corroborated the protistan origination and heterogeneous distribution of the contaminated contigs. Overall, in this study, we conducted a large-scale scan of protistan contaminant in genomic resources, and the protistan sequences detected will help uncover the protist diversity and relationships of these picoeukaryotes with Metazoa. Full article

The oligotrophy of the southern Adriatic Sea is characterized by seasonal stratification which enables nutrient supply to the euphotic layer. A set of interdisciplinary methods was used to elucidate the diversity and co-dependency of bacterio- and phytoplankton of the water column during the stratification period of July 2021. A total of 95 taxa were determined by microscopy: 58 diatoms, 27 dinoflagellates, 6 coccolithophores, and 4 other autotrophs, which included Chlorophyceae, Chrysophyceae, and Cryptophytes. Nanophytoplankton abundances were higher in comparison to microphytoplankton. The prokaryotic plankton community as revealed by HTS was dominated by Proteobacteria (41–73%), Bacteroidota (9.5–27%), and cyanobacteria (1–10%), while the eukaryotic plankton community was composed of parasitic Syndiniales (45–80%), Ochrophyta (2–18%), Ciliophora (2–21%), Chlorophytes (2–4%), Haptophytes (1–4%), Bacillariophyta (1–13%), Pelagophyta (0.5–12%) and Chrysophyta (0.5–3%). Flow cytometry analysis has recorded Prochlorococcus and photosynthetic picoeukaryotes as more abundant in deep chlorophyll maximum (DCM), and Synechococcus and heterotrophic bacteria as most abundant in surface and thermocline layers. Surface, thermocline, and DCM layers were distinct considering community diversity, temperature, and nutrient correlations, while extreme nutrient values at the beginning of the investigating period indicated a possible nutrient flux. Nutrient and temperature were recognized as the main environmental drivers of phytoplankton and bacterioplankton community abundance. Full article

The CHEMTAX program has been widely used to estimate community composition based on major pigment concentrations in seawater. However, because CHEMTAX is an underdetermined optimization algorithm, underdetermined bias has remained an unsolved problem since its development in 1996. The risk of producing biased results increases when analyzing the picophytoplankton community; therefore, this study tested a new method for avoiding biased CHEMTAX results using the picophytoplankton community around the East Sea (Japan Sea). This method involves building a linear model between pigment concentration data and community composition data based on DNA sequencing to predict the pigment range for each operational taxonomic unit, based on the 95% prediction interval. Finally, the range data are transformed into an initial ratio and ratio limits for CHEMTAX analysis. Three combinations of initial ratios and ratio limits were tested to determine whether the modeled initial ratio and ratio limit could prevent underdetermined bias in the CHEMTAX estimates; these combinations were the modeled initial ratio and ratio limit, the modeled initial ratio with a default ratio limit of 500 s, and an initial ratio from previous research with the default ratio limit. The final ratio and composition data for each combination were compared with Bayesian compositional estimator-based final ratio and composition data, which are robust against underdetermined bias. Only CHEMTAX analysis using the modeled initial ratio and ratio limit was unbiased; all other combinations showed significant signs of bias. Therefore, the findings in this study indicate that ratio limits and the initial ratio are equally important in the CHEMTAX analysis of biased datasets. Moreover, we obtained statistically supported initial ratios and ratio limits through linear modeling of pigment concentrations and 16s rDNA composition data. Full article

Biological organic carbon production and consumption play a fundamental role in the understanding of organic carbon cycling in oceans. However, studies on them in the Kuroshio, the western boundary current in the North Pacific Ocean, are scarce. To better understand the variations of plankton community respiration (CR) and particulate organic carbon (POC), eight cruises. which covered four seasons over a 2-year period, were surveyed across the Kuroshio at the KTV1 transect east of Taiwan. Spatially, a coastal uplift of isotherms (i.e., onshore lifting and offshore deepening) was observed along the KTV1 transect. During the uplift, the cold and nutrient-rich deep waters shoal to shallow water and enhance phytoplankton growth, resulting in higher values of phytoplankton, POC, and plankton CR on the onshore side. In this study, phytoplankton was dominated by picophytoplankton including Prochlorococcus, Synechococcus, and picoeukaryotes. Plankton CR was low, and its mean depth-normalized integrated rate (the upper 100 m water depth) ranged from 7.07 to 22.27 mg C m⁻³ d⁻¹, to which the picophytoplankton and heterotrophic bacteria contributed the most. The mean depth-normalized integrated value of POC ranged from 12.7 to 21.6 μg C L⁻¹. POC is mainly associated with phytoplankton biomass with a mean carbon ratio of chlorophyll a/POC ≈ 1.03. All results suggest that plankton CR and POC variations may be associated with picoplankton dynamics in the Kuroshio. Full article

Picophytoplankton (pico) in the eastern Indian Ocean (EIO) were investigated during the inter-monsoon periods. They were found to typically comprise Prochlorococcus (Pro), Synechococcus (Syn), and Picoeukaryotes (PEuks). In the survey area, the pico showed two different vertical distribution patterns in different regions, whereby the Syn abundance decreased with depth, whereas those of Pro and PEuks increased and then decreased with depth, with the maximum depths ranging from 50 to 100 m. The cell abundance and community structure of the pico were similar at the equator (EQ) and the eastern boundary of the Indian Ocean near Sumatra (EB), but the pico cell abundance was significantly lower in the Bay of Bengal (BOB). Pro dominated most regions of the entire EIO and were approximately one-to-two orders of magnitude more abundant than Syn and PEuks. The distributions of Syn and PEuks showed little difference across various regions. Influenced by the physicochemistry of circulation and water masses, there were many different environmental factors in the different regions. The abundance of pico domination by Pro showed a strong positive correlation with the nutrients and salinity in the survey area, indicating increasing nutrient availability, particularly in the oligotrophic EIO. Generalized additive models (GAMs) analysis showed the differences in their responses to environmental variability. Pro and PEuks both increased strongly with warming up to below 26 °C, and Pro and PEuks were more responsive to chemical (nutrient) variability. Syn showed a broader tolerance of low-salinity conditions. In a certain range, an increase in nitrite and nitric acid can improve the cell abundance of Pro. As a significant contributor to primary productivity in oligotrophic waters, this study provides essential information for studying pico communities in the EIO and its adjacent marine ecosystems. Full article

Critical questions exist regarding the abundance and, especially, the export of picophytoplankton (≤2 µm diameter) in the Arctic. These organisms can dominate chlorophyll concentrations in Arctic regions, which are subject to rapid change. The picoeukaryotic prasinophyte Micromonas grows in polar environments and appears to constitute a large, but variable, proportion of the phytoplankton in these waters. Here, we analyze 81 samples from the upper 100 m of the water column from the Fram Strait collected over multiple years (2009–2015). We also analyze sediment trap samples to examine picophytoplankton contributions to export, using both 18S rRNA gene qPCR and V1-V2 16S rRNA Illumina amplicon sequencing to assess the Micromonas abundance within the broader diversity of photosynthetic eukaryotes based on the phylogenetic placement of plastid-derived 16S amplicons. The material sequenced from the sediment traps in July and September 2010 showed that 11.2 ± 12.4% of plastid-derived amplicons are from picoplanktonic prasinophyte algae and other green lineage (Viridiplantae) members. In the traps, Micromonas dominated (83.6 ± 21.3%) in terms of the overall relative abundance of Viridiplantae amplicons, specifically the species Micromonas polaris. Temporal variations in Micromonas abundances quantified by qPCR were also observed, with higher abundances in the late-July traps and deeper traps. In the photic zone samples, four prasinophyte classes were detected in the amplicon data, with Micromonas again being the dominant prasinophyte, based on the relative abundance (89.4 ± 8.0%), but with two species (M. polaris and M. commoda-like) present. The quantitative PCR assessments showed that the photic zone samples with higher Micromonas abundances (>1000 gene copies per mL) had significantly lower standing stocks of phosphate and nitrate, and a shallower average depth (20 m) than those with fewer Micromonas. This study shows that despite their size, prasinophyte picophytoplankton are exported to the deep sea, and that Micromonas is particularly important within this size fraction in Arctic marine ecosystems. Full article

The extreme environmental conditions of the diverse saline inland waters (soda lakes and pans, hypersaline lakes and ponds) of the Carpathian Basin are an advantage for picophytoplankton. The abundance of picophytoplankton in these waters can be up to several orders of magnitude higher than that in freshwater shallow lakes, but differences are also found within different saline water types: higher picophytoplankton abundances were observed in hypersaline lakes compared to humic soda lakes, and their highest numbers were detected in turbid soda lakes. Moreover, their contribution to phytoplankton biomass is higher than that in shallow freshwater lakes with similar trophic states. Based on long-term data, their ratio within the phytoplankton increased with turbidity in the case of turbid soda lakes, while, in hypersaline lakes, their proportion increased with salinity. Picocyanobacteria were only detected with high abundance (>10⁶–10⁷ cells/mL) in turbid soda lakes, while picoeukaryotes occurred in high numbers in both turbid and hypersaline lakes. Despite the extreme conditions of the lakes, the diversity of picophytoplankton is remarkable, with the dominance of non-marine Synechococcus/Cyanobium, Choricystis, Chloroparva and uncultured trebouxiophycean green algae in the soda lakes, and marine Synechococcus and Picochlorum in the hypersaline lakes. Full article

Phaeocystis globosa blooms frequently in the Beibu Gulf of China. This species has a distinct life cycle that includes colonies and solitary cells. Colonies are formed during a bloom, while solitary cells are produced between blooms. Information about the abundance of solitary cells and other picophytoplankton in the northern Beibu Gulf is limited. To elucidate phytoplankton variation trends during periods of frequent P. globosa blooms and to determine the main physiochemical factors affecting phytoplankton distribution, four cruises were conducted between November 2018 and April 2019. Seawater was collected, and water temperature, salinity, and nutrient concentrations were simultaneously determined. Redundancy analysis was performed to understand the relationship between environmental factors and phytoplankton assemblages. Seven phytoplankton clusters were present during the cruises. Picophytoplankton abundance (including Synechococcus and Picoeukaryote groups I and II) dominated during the four cruises. Synechococcus abundance was restricted by the low temperatures in winter, decreasing from November to February and increasing in April. Picoeukaryote I abundance was almost unaffected by low temperatures and was mainly affected by nutrient concentration. P. globosa solitary cell abundance increased from November to January and decreased in February and April, and phosphorus was the key factor affecting P. globosa blooms. This is the first study to reveal the abundance and distribution of P. globosa solitary cells in this area. Full article

The circadian clock orchestrates an organism’s endogenous processes with environmental 24 h cycles. Redox homeostasis and the circadian clock regulate one another to negate the potential effects of our planet’s light/dark cycle on the generation of reactive oxygen species (ROS) and attain homeostasis. Selenoproteins are an important class of redox-related enzymes that have a selenocysteine residue in the active site. This study reports functional understanding of how environmental and endogenous circadian rhythms integrate to shape the selenoproteome in a model eukaryotic cell. We mined quantitative proteomic data for the 24 selenoproteins of the picoeukaryote Ostreococcus tauri across time series, under environmentally rhythmic entrained conditions of light/dark (LD) cycles, compared to constant circadian conditions of constant light (LL). We found an overrepresentation of selenoproteins among rhythmic proteins under LL, but an underrepresentation under LD conditions. Rhythmic selenoproteins under LL that reach peak abundance later in the day showed a greater relative amplitude of oscillations than those that peak early in the day. Under LD, amplitude did not correlate with peak phase; however, we identified high-amplitude selenium uptake rhythms under LD but not LL conditions. Selenium deprivation induced strong qualitative defects in clock gene expression under LD but not LL conditions. Overall, the clear conclusion is that the circadian and environmental cycles exert differential effects on the selenoproteome, and that the combination of the two enables homeostasis. Selenoproteins may therefore play an important role in the cellular response to reactive oxygen species that form as a consequence of the transitions between light and dark. Full article

Seasonal variations in the picophytoplankton community structure (Synechococcus spp. and picoeukaryotes) were studied by flow cytometry in the coastal ecosystem of the subtropical western Pacific from October 2019 to September 2020. Synechococcus spp. was dominant in abundance during the study period, with its density ranging from 0.05 to 5.6 × 10⁴ cells mL⁻¹; its maximum occurred in July 2020. Picoeukaryotes were less abundant, with their density ranging from 0.2 to 13.6 × 10³ cells mL⁻¹. Their highest abundance was recorded in January 2020. The growth rates of Synechococcus spp. and picoeukaryotes ranged from −0.39 to 1.42 d⁻¹ and 0.38 to 2.46 d⁻¹, respectively, throughout the study period. Overall, the growth rate of the picoeukaryotes was significantly higher than that of Synechococcus spp. It is interesting to note that the grazing mortality of Synechococcus spp. and picoeukaryotes during the warmer period (April to September) was relatively low. Based on this study, we suggest that mixotrophic nanoflagellates lowered their feeding activity that obtained nutrients from prey and instead used additional nutrients during the incubation experiments. Our study demonstrated that a shift in the picophytoplankton community composition and grazing activity of predacious nanoflagellates in cold and warm periods can impact on the seasonal dynamics of the microbial food web. Full article

A remarkable shift in the species composition and size distribution of the phytoplankton community have been observed in coastal waters along the Antarctic Peninsula over the last three decades. Smaller photoautotrophs such as cryptophytes are becoming more abundant and important for the regional ecosystems. In this study, flow cytometry was used to quantify the smallest phytoplankton in the central Bransfield Strait and explore their distribution across the strait in relation to physical and chemical properties of the two major water masses: the warmer and less saline Transitional Zonal Water with Bellingshausen Sea influence (TBW), and the cold and salty Transitional Zonal Water with Weddell Sea influence (TWW). Pico- and nano-phytoplankton clusters were distinguished and enumerated in the cytograms: photosynthetic picoeukaryotes, cryptophytes (about 9 µm in size), and smaller (3 µm) nanophytoplankton. It was shown that nanophytoplankton developed higher abundances and biomasses in the warmer and less saline TBW. This biotope was characterized by a more diverse community with a pronounced dominance of Cryptophyta in terms of biomass. The results support the hypothesis that increasing melt-water input can potentially support spatial and temporal extent of cryptophytes. The replacement of large diatoms with small cryptophytes leads to a significant shift in trophic processes in favor of the consumers such as salps, which able to graze on smaller prey. Full article

In this study, flow cytometry (FCM) and size-fractionated filtration, together with high-throughput molecular sequencing methods (SM), were used to investigate picophytoplankton. A particle separation filter and a higher-throughput sequencing method were used to evaluate the composition of a euphotic zone of picophytoplankton—especially picoeukaryotic phytoplankton—in the Western Pacific, and the results of flow cytometry, which is a classic way to detect picophytoplankton, were used as a standard to evaluate the reliability of the results of the SMs. Within a water column of 200 m, six water depths (5, 25, 50, 113 (DCM), 150, and 200 m) were established. In order to further study the particle size spectra of the picophytoplankton, size-fractionated filtration was used to separate water samples from each water depth into three particle size ranges: 0.2–0.6, 0.6–1.2, and 1.2–2 $\mathsf{\mu }$m. A total of 36 (6 × 3 × 2) samples were obtained through PCR amplification of the 18S rRNA V4 hypervariable region and 16S rRNA, which were biased toward phytoplankton plastids, and then high-throughput sequencing was performed. The estimation of the picophytoplankton diameter relied on forward scattering (FSC) through FCM. The estimation of the vertical distribution and diameter of the picophytoplankton using the SM was consistent with the results with FCM; thus, we believe that the estimation of picophytoplankton composition with the SM has value as a reference, although the size-fractionated filtration seemed to cause some deviations. In addition to Prochlorococcus and Synechococcus, the SM was used to evaluate the composition of picoeukaryotic phytoplankton, which mainly included Prymnesiophycea (Haptophyta) (38.15%), Cryptophyceae (Cryptophyta) (22.36%), Dictyochophyceae (Chrysophyta) (12.22%), and Mamiellophyceae (Chlorophyta) (3.31%). In addition, the SM also detected Dinophyceae (Dinoflagellata) (11.69%) sequences and a small number of Bacillariophyceae (Diatom) (1.64%) sequences, which are generally considered to have large particle sizes. The results of the SM also showed that the picoeukaryotic phytoplankton were not evenly distributed in the euphotic layer, and the vertical distributions of the different picoeukaryotic phytoplankton were different. An analysis of correlations with environmental factors showed that temperature was the main environmental factor controlling the vertical distribution of picophytoplankton. Full article